Related Experiment Video
Updated: Nov 1, 2025
Identification of Circular RNAs using RNA Sequencing
Published on: November 14, 2019
Bioinformatic Analysis of Circular RNA Expression
Enrico Gaffo1, Alessia Buratin1,2, Anna Dal Molin1
1Department of Molecular Medicine, University of Padova, Padova, Italy.
Abstract:
Circular RNAs (circRNAs) are stable RNA molecules generated by backsplicing that play regulatory functions through interaction with other RNA and proteins, as well as by encoding peptides. Dysregulation of circRNA expression can drive cancer development and progression with different mechanisms. CircRNAs are currently regarded as extremely attractive molecules in cancer research for the identification of new and possibly targetable disease regulatory networks and for the development of biomarkers for cancer diagnosis, prognosis definition, and monitoring. Using specific experimental and computational protocols, circRNAs can be identified through RNA-seq by spotting the reads spanning backsplice junctions, which are specific to circular molecules. In this chapter, we report a state-of-the-art computational protocol for a genome-wide analysis of circRNAs from RNA-seq data, which considers circRNA detection, quantification, and differential expression testing. Finally, we indicate how to determine circular transcript sequences and the resources for an in silico functional characterization of circRNAs.
Insights
Circular RNAs (circRNAs) are key regulators in cancer. This study presents a computational protocol for analyzing circRNA expression from RNA-seq data, aiding cancer research and biomarker development.
Area of Science:
- Molecular Biology
- Bioinformatics
- Cancer Research
Background:
- Circular RNAs (circRNAs) are generated by backsplicing and regulate gene expression.
- Dysregulated circRNA expression is implicated in cancer development and progression.
- circRNAs hold potential as cancer biomarkers and therapeutic targets.
Purpose of the Study:
- To present a state-of-the-art computational protocol for genome-wide circRNA analysis.
- To enable accurate detection, quantification, and differential expression testing of circRNAs.
- To guide the determination of circular transcript sequences and in silico functional characterization.
Main Methods:
- Utilizing RNA-sequencing (RNA-seq) data.
- Identifying circRNAs by detecting reads spanning backsplice junctions.
- Employing computational protocols for genome-wide analysis.
Main Results:
- A comprehensive protocol for circRNA analysis from RNA-seq data is provided.
- The protocol facilitates circRNA detection, quantification, and differential expression analysis.
- Methods for determining circular transcript sequences and functional characterization are outlined.
Conclusions:
- The presented computational protocol is valuable for advancing circRNA research in cancer.
- This approach supports the identification of novel cancer regulatory networks.
- The protocol aids in the development of circRNA-based biomarkers for cancer diagnosis and monitoring.
Related Concept Videos
03:21RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
02:24Ribosome Profiling
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
02:28Leaky Scanning